Re: [phenixbb] Fucose alpha linkage

Dear Nigel and others, I had reported a while ago that the phenix ALPHA1-3 linkage will convert the a-L-fucose to have a beta anomer. Actually, it was even worse; at the time the monomer library had the beta-L-fucose under the FUC-a-L entry. http://www.mail-archive.com/[email protected]/msg13968.html At the time, I had even created a flickr site to show the problem: http://www.flickr.com/photos/46544052@N03/4274285327/ It has been a while since I thought about this, but I think that this happens specifically with L-Fucose (all other standard N-linked sugars, I believe they are D-sugars, are fine). Since this was not resolved at the time, I have resorted to this workaround: Use your own FUC.cif, where you are sure that the C1 chiral center is alpha. Use BETA1-3, BETA1-6 linkages to enforce alpha linkages. I hope my memory is serving me right on this. Since then, CNS 1.3 has incorporated the correct linkages. Please see the carbohydrate.top file in your CNS installation. There, on top of A13 and A16, there are separate A13L and A16L linkages for FUC (I guess L stands for L-sugars, which applies only to Fucose). I would really love to see this corrected in Phenix and CCP4 monomer libraries (if it has already been fixed, thank you!). Cheers, Engin P.S. Here is how CNS 1.3 does N-linked linkages: REMARKS B1N: N-linked glycan beta link from NAG and NDG to ASN (asparagine) ! note: PDB files with unusual NDG to ASN links are likely incorrect assignments ! they will be forced into the beta anomer by the B1N link. REMARKS B12: beta(1,2) link from BGC, GAL, BMA, NAG, FCB, XYP to any REMARKS B14: beta(1,4) link from BGC, GAL, BMA, NAG, FCB, XYP to any REMARKS A12: alpha(1,2) link from GLC, GLA, MAN, NDG, A2G, FCA to any REMARKS A13: alpha(1,3) link from GLC, GLA, MAN, NDG, A2G, FCA to any REMARKS A14: alpha(1,4) link from GLC, GLA, MAN, NDG, A2G, FCA to any REMARKS A16: alpha(1,6) link from GLC, GLA, MAN, NDG, A2G, FCA to any REMARKS B12L: beta(1,2) link from FUL to any REMARKS B14L: beta(1,4) link from FUL to any REMARKS A12L: alpha(1,2) link from FUC to any REMARKS A13L: alpha(1,3) link from FUC to any REMARKS A14L: alpha(1,4) link from FUC to any REMARKS A16L: alpha(1,6) link from FUC to any REMARKS A23: alpha(2,3) link from GAL to SIA REMARKS A26: alpha(2,6) link from GAL to SIA On 11/29/11 3:30 PM, Nigel Moriarty wrote:

Tim

The glycosidic bonds in PHENIX are taken from the Monomer Lib so I think that should be OK.

O1 can be in the axial or equatorial position depending on the ring pucker but the O1 should always be on the opposite side of the ring (if you imagine the ring is flattened) from the C6. It is the chirality around the C1 atom that specifies the alpha/beta linkage. Please send me the PDB file (off-line) so I can double-check that it is correct. Just the three carbohydrate residues would be fine.

Cheers

Nigel

On Tue, Nov 29, 2011 at 3:13 PM, Timothy Springer wrote:

...

Hi, I have just added alpha1-3 and alpha1-6 fucoses to NAG. The Fucose in the monomer library has O1 in the alpha position, which is axial. However, after refinement, the fucose moves so it is linked beta in the equatorial position. I believe the alpha and beta linkages for Fucose may be reversed in Phenix. Please advise. The links are below.

apply_cif_link { data_link = "ALPHA1-3" residue_selection_1 = "chain A and resname NAG and resid 3821" residue_selection_2 = "chain A and resname FUC and resid 3824" } apply_cif_link { data_link = "ALPHA1-6" residue_selection_1 = "chain A and resname NAG and resid 3821" residue_selection_2 = "chain A and resname FUC and resid 3823" }

With my best regards, Tim Timothy A. Springer, Ph.D. Latham Family Professor of Biological Chemistry and Molecular Pharmacology

Harvard Medical School http://idi.harvard.edu/springer Immune Disease Institute [email protected] Program in Cellular and Molecular Medicine, Dept. Medicine Div. Hematology Children's Hospital Boston 3 Blackfan Circle, Rm 3103 phone: 617-713-8200 Boston MA 02115 fax: 617-713-8232

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